AVMCD:基于16S rRNA测序的微生物群落多样性分析与可视化平台
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摘要
传统的技术手段已逐渐难以适应现代生物技术的发展,随着以16S rRNA为代表的第二代高通量测序技术飞速发展,微生物群落多样性研究已进入分子时代,但要分析庞大的测序数据并从中找寻存在的关联还是给生物学家带来诸多现实困难.为帮助研究者更快更好地掌握微生物群落多样性的信息,开发了AVMCD(analysis and visualization of microbial community datasets)生物信息平台,提供基于16S rRNA测序的专业在线分析及可视化服务.AVMCD坚持友好快捷的交互方式,注册用户只需上传待分析的数据,根据提示简单设置参数,即可由平台自动展开专业的序列分析,并将结果以丰富的可视化形式呈现给用户.
Traditional techniques have gradually become difficult to adapt to the development of modern biotechnology.With the rapid development of next-generation high-throughput sequencing technology about 16 S rRNA,the study of microbial community diversity has entered the molecular age.To help researchers understand the information of microbial community diversity quickly,a bioinformatics platform called AVMCD has been developed for providing registered users with professional analysis and visualization services based on 16 S rRNA sequence online.The aim of AVMCD is to create a mode which makes the interaction more convenient and friendly.Users only need upload the data set to be analyzed and set the parameters according to prompts,then the platform can automatically begin the sequencing analysis professionally and present all the results in a rich form of visualization.
Traditional techniques have gradually become difficult to adapt to the development of modern biotechnology.With the rapid development of next-generation high-throughput sequencing technology about 16 S rRNA,the study of microbial community diversity has entered the molecular age.To help researchers understand the information of microbial community diversity quickly,a bioinformatics platform called AVMCD has been developed for providing registered users with professional analysis and visualization services based on 16 S rRNA sequence online.The aim of AVMCD is to create a mode which makes the interaction more convenient and friendly.Users only need upload the data set to be analyzed and set the parameters according to prompts,then the platform can automatically begin the sequencing analysis professionally and present all the results in a rich form of visualization.
引文
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[14] 王利松,陈彬,纪力强,等.生物多样性信息学研究进展 [J].生物多样性,2010,18(5):429-443.
[15] 杨立娜,黄靖航,赵亚凡,等.胃肠道体外模拟系统在调控肠道菌群研究中的应用进展[J].渤海大学学报(自然科学版),2018,39(4):320-329.
[16] Tom Hughes-Croucher,Mike Wilson,郑达韡.Node即学即用 [M].北京:人民邮电出版社,2013:2-1.
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[2] 刘驰,李家宝,芮俊鹏,等.16S rRNA 基因在微生物生态学中的应用[J].生态学报,2015,35(9):2769-2788.
[3] 龙雯,陈存社.16S rRNA测序在细菌鉴定中的应用 [J].北京工商大学学报,2006,24(5):10-12.
[4] Ludwig W O,Strunk R,Westram L,et al.ARB:a software environment for sequence data[J].Nucleic Acids Res,2004,32:1363-1371.
[5] Schloss P D,Handelsman J.Introducing DOTUR,a computer program for defining operational taxonomic units and estimating species richness[J].Appl.Environ.Microbiol,2005,71:1501-1506.
[6] Schloss P D,Handelsman J.Introducing SONS,a tool that compares the membership of microbial communities[J].Appl.Environ.Microbiol,2006,72:6773-6779.
[7] Singleton D R.,Furlong M A,Rathbun S L,et al.Whitman.Quantitative comparisons of 16S rRNA gene sequence libraries from envi-ronmental samples[J].Appl.Environ.Microbiol,2001,67:4374-4376.
[8] Lozupone C,Knight R.UniFrac:a new phylogenetic method for comparing microbial communities.Appl.Environ.Microbiol,2005,71:8228-8235.
[9] Martin A P.Phylogenetic approaches for describing and comparing the diversity of microbial communities[J].Appl.Environ.Microbiol,2002,68:3673-3682.
[10] Schloss P D,Handelsman J.Introducing TreeClimber,a test to compare microbial community structure[J].Appl.Environ.Microbiol,2006,72:2379-2384.
[11] Cole J R.,Wang Q,Cardenas E,et al.The Ribosomal Database Project:improved alignments and new tools for rRNA analysis[J].Nucleic Acids Res,2009,37:141-145.
[12] Patrick D S,Sarah L W,Thomas R,et al.Introducing mothur:Open-Source,Platform-Independent,Community-Supported Software for Describing and Comparing Microbial Communities[J].Appl.Environ.Microbiol,Dec,2009:7537-7541
[13] Caporaso J G,Kuczynski J,Stombaugh J,et al.QIIME allows analysis of high-throughput community sequencing data.Nat Meth,2010,7(5):335-336.
[14] 王利松,陈彬,纪力强,等.生物多样性信息学研究进展 [J].生物多样性,2010,18(5):429-443.
[15] 杨立娜,黄靖航,赵亚凡,等.胃肠道体外模拟系统在调控肠道菌群研究中的应用进展[J].渤海大学学报(自然科学版),2018,39(4):320-329.
[16] Tom Hughes-Croucher,Mike Wilson,郑达韡.Node即学即用 [M].北京:人民邮电出版社,2013:2-1.
[17] Ethan Brown.吴海星,苏文译.Node与Express开发[M].北京:人民邮电出版社,2015:2-2.
[18] 付琳林,李海星.利用变性梯度凝胶电泳分析微生物的多样性[J].生物技术通报,2004(2):37-40.